


Compromised Positions

by Tarlan



Series: Strange Changes [2]
Category: Stargate Atlantis
Genre: Alpha/Beta/Omega Dynamics, Angst, Community: mpregbigbang, M/M, Mpreg, Trope Bingo Round 3
Language: English
Status: Completed
Published: 2014-03-08
Updated: 2014-03-08
Packaged: 2018-01-13 09:54:33
Rating: Explicit
Warnings: No Archive Warnings Apply
Chapters: 1
Words: 10,271
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/1221889
Author URL: https://archiveofourown.org/users/Tarlan/pseuds/Tarlan
Summary: <blockquote class="userstuff">
              <p>When Atlantis returned to Pegasus after saving Earth from the Wraith Superhive ship, no one noticed the strange changes taking place, especially to those with the ATA gene either naturally or through Carson Beckett's gene therapy. By the time the Daedalus arrived, Atlantis had not only altered the physiology of those in the city but had also stripped them of their emotional connection to their home world. But not everyone was happy with the changes and so Carson developed a cure. As a man, John had never been happier in his life. He had a home, his new family... and he had his bonded mate, Rodney. As a soldier, John knew he was compromised and it was his duty to take the cure, and somehow live with the consequences.</p>
            </blockquote>





	Compromised Positions

**Author's Note:**

  * For [popkin16](https://archiveofourown.org/users/popkin16/gifts), [marlislash](https://archiveofourown.org/users/marlislash/gifts), [Gryph](https://archiveofourown.org/users/Gryph/gifts).
  * Inspired by [Art and Fanmix for "Compromised Positions"](https://archiveofourown.org/works/1215589) by [Gryph](https://archiveofourown.org/users/Gryph/pseuds/Gryph). 



> Written for **MPregBigBang** 2013-14  
>  and also meets **trope_bingo** Round 3: mind control
> 
>  **Thank you to AQUALEGIA** for giving the story a final read-through :)
> 
>  **With many, many thanks for the wonderful art and fantastic fanmix by Gryph (gryphon2k)** \- due to International time differences, please check back later if the fanmix link is not yet available! It should be there within the next 12 hours.
> 
> I've also gifted this to **Popkin16** and **Marlislash** as a thank you for all their wonderful support for my stories and art. THANK YOU!

John smiled as he watched Rodney's hands flying, not needing to hear the words to know Rodney was excited over Gorman's latest discovery. He focused inwards, feeling the slender bond stretching between them that proved it really was excitement rather than anger governing Rodney's emotions right now. His smile grew fonder, with warmth coiling through him as he recalled how he had woken that very morning to the welcome weight of Rodney sprawled half across him.

He'd awoken that same way every morning since the incident in the mess hall - when the touch of Rodney's hand had ignited something so deep and desperate within him that others had been forced to drag them apart before he consummated that need in front of everyone present. He shuddered in memory of Rodney's cry of pain as they were torn apart, aware now that it had been a side effect from the strange changes that meant Rodney could no longer stand the touch of anyone else except for him. He could still recall the intense rage that had consumed him at Rodney's pain-filled cry, and the sickening crunch of his fist breaking Corporal Hillson's cheekbone as he launched himself at those daring to touch Rodney - before he was hit with a stun blast from Ronon's gun.

Whatever it was, the intense emotions and Rodney's painful response to touch had worn off by the time they left the isolation room a few days later, fully bonded. Carson believed it was some form of pre-bond link that made the omega - as Carson called them - extremely sensitive to the touch of only the intended alpha, and the alpha intensely aware and possessive of his or her intended omega mate.

John knew that he and Rodney were not the only ones who had experienced the intensity of the bonding over the week that followed, necessitating new rules when dealing with pre-bonded couples. Fortunately, very few of the alpha-omega pairs were caught out in such a public area and everyone was given orders to simply back off and seal them away until they had finalized the bond, even if it meant abandoning a lab for the duration - as long as it posed no danger to either the pair, to anyone else in the city, or to Atlantis.

Where it was deemed necessary, a Wraith stunner or Ronon's blaster set to stun resolved the issue quickly and painlessly for all concerned.

By the end of that week, only a handful of alphas and omegas were left unbonded. Whatever chemistry had brought the other pairs together seemed to be missing from these individuals, and John could almost sense their unbonded state. It was like a bone-deep emptiness, and he recognized it for how he had felt only a week earlier. Rodney had filled that void within him with his living, breathing presence. Every brush of his hand or caress of his mind shimmered in the fine, golden thread linking them together.

John sipped at his coffee and smirked as Rodney registered John's thoughts as a caress upon his own mind, half turning to glance quickly in John's direction.

It was hard to believe that the bond between them had existed for only a week because it felt as if they had always been together. Or perhaps it just seemed that way because they had been friends for a long time before Atlantis altered them genetically. After just one week John could no longer imagine going back to how it was before. The bond had soothed a loneliness that John hadn't even recognized until it was no longer there, and for the first time in his life he felt whole - complete - and he knew Rodney felt the same too.

Ronon dropped down in the seat opposite and John rolled his eyes because Ronon hadn't stopped smirking at him since the _incident_ , taking great pleasure in reminding John that he'd had to stun him... again... and the reason why.

"Not the first time I've had to shoot you."

"Yeah, and I'm beginning to think you like doing that a little _too_ much."

The smirk widened, becoming a wide, toothy grin that bordered on feral. "Figured you'd prefer that to-."

"Yeah," John grimaced. "Thanks. Again."

"Welcome." Ronon dug into his meal taking several large mouthfuls before looking back up at John from under far shorter hair that lacked the dreadlocks that had framed his face for so long. "McKay?" He smirked again, shaking his head. "Should have seen that one."

Deciding he needed to change the subject, John indicated towards Ronon.

"What happened to the hair?"

"Not that man anymore."

John nodded, because he understood what Ronon meant. They were different now. Even the ones who had gone through only a small genetic alteration could feel the difference both mentally and physically, though not everyone was content with the changes forced upon them. He knew that many of the weaker ATA gene carriers resented not gaining alpha or even omega status, while a few of the pure humans were disgruntled that these changes would make it impossible for them to go back to Earth.

A message came through and he tapped his radio.

"Sheppard."

"The _Daedalus_ will be moving into Geo-synchronous orbit shortly, sir."

John glanced first at Ronon and then across the room to where Rodney had stopped and was looking at him, one hand raised to his ear. Rodney nodded.

"We're on our way," John responded.

****

The arrival of the _Daedalus_ caused a stir especially when Woolsey refused to grant Caldwell permission to land. Atlantis had been out of contact with Earth and Stargate Command for almost two weeks now so Caldwell wasn't aware of the radical new development in the genetic changes that had overcome the New Lanteans. It didn't take long to explain the situation, and he wisely chose to remain in orbit rather than landing on the South Pier and risking his crew becoming affected by whatever Atlantis was doing to its people.

Woolsey set up a video conference in the main briefing room, and John took his customary seat opposite Rodney despite the temptation to sink down next to his... He paused at that thought, still unsure what he should call Rodney. His partner? Mate? Bondmate? He had heard several new terms - some endearing like soulmate, others derogatory, calling the omega his bitch - and wondered what they would settled on eventually.

"So let me get this straight," Caldwell stated. "Everyone in Atlantis has been... compromised by the city's A.I."

Rodney huffed. "Well, compromised might be too strong a term-."

"No, Rodney," John interrupted. "He's right. We've all been compromised even if it doesn't feel that way to us. Our memories of...," he struggled to recall the name of his home planet, "Earth... lack an emotional connection, so our loyalty to Earth and Stargate Command is questionable at the very least."

"Or nonexistent," Lorne muttered. "I feel as much connection with Earth as I do with Manaria."

John grimaced. "Exactly my point."

"Then I have no option but to relieve you of command, Colonel Sheppard."

Rodney's chair scraped back as he stood up in shock. "What! No! Your military has no jurisdiction here on Atlantis. You can't-."

John had stood too, along with Lorne. "Rodney," he snapped out but sent reassurance through their shared link, staring hard at him until Rodney sank back down into his seat, arms crossed over his chest in annoyance. "Colonel Caldwell is following the correct protocol. I can't remain in command of _Earth_ 's forces on Atlantis."

It took a moment longer before Rodney blinked rapidly, finally letting the fog of frustration and anger fade enough to understand what John was saying. As John retook his seat, Woolsey spoke up.

"I concur with you both. The current Earth military on Atlantis can no longer be commanded by Colonel Sheppard. Sergeant Barat will assume command in the interim."

Barat, who had remained quiet for the duration of the meeting so far, stood up and saluted. John could tell from whatever scent or vibes he gave off that Barat was one of the weaker betas who was still practically human. His presence in the briefing room proved that Woolsey was already one step ahead and John watched as Woolsey clasped his hands together on the table in front of him, continuing before Rodney could object again.

"However, I am appointing Colonel Sheppard as the commanding officer for the _Lantean_ military on Atlantis, with Major Lorne as his second in command."

Caldwell nodded tightly, and John nodded back in acceptance, inwardly smiling.

When Woolsey was first appointed as the civilian head of Atlantis, representing the I.O.A., John had his doubts about him, seeing Woolsey as the worst kind of pen pusher, but over the years he had proved to be a great leader. Once again, John wished Carson had figured out a better naming system for these changes because beta did seem to imply _second_ ; second class, weaker. 

Perhaps to Atlantis the betas were of lesser importance than those with strong expressions of the ATA gene, but not to John. As a human Woolsey had not had the ATA gene naturally, and the gene therapy had not worked on him making him a beta now, but he still retained a strength of resolve that proved that betas were just as strong willed as those whom Atlantis had made alphas and omegas, and more than capable of taking leadership positions within the city.

Caldwell sighed, lips twisting slightly in distaste. "Under the circumstances, I suppose there is little point asking you to step aside as civilian leader on Atlantis, Mr. Woolsey."

Woolsey smiled and tilted his head in acknowledgment. "And under the circumstances, you are correct. The I.O.A. no longer has any jurisdiction within the city either, but I would be remiss if I didn't consider a small number of Lanteans who are not so enamored with our current... circumstances. Perhaps Doctor Beckett can share his findings."

John knew Carson was close to producing a retrovirus to counteract the changes for those who fell into the main group - the betas - so he listened intently as Carson outlined his plans to start his testing by switching off the changes made to those who had never had the ATA gene. It meant that those least affected by the strange changes introduced by Atlantis could return to Earth if they so wished. John glanced across the table at Sergeant Barat, wondering whether he would take Carson's ' _cure_ '.

The meeting came to an end and John hung back, wanting to speak with Woolsey alone.

"Richard?"

"John. I'll need to make the necessary announcements."

"You know there'll be a few with divided loyalties... to both Earth and to Atlantis."

"Unfortunately there is little I can do except tell the truth and allow them to make their own decisions."

"And I agree with you, but not everyone is going to _like_ the decisions that others make."

"And that's where you and Sergeant Barat will have to work together, and be vigilant."

John chewed on his lower lip thoughtfully. "Would you take Carson's retrovirus?" John asked.

Woolsey looked away for a moment, expression serious when he looked back. "John, I was offered a lucrative position within the I.O.A. while on Earth, but I made my decision when I turned it down to stay on Atlantis. I know my own mind already. However, I am aware that the... alphas and omegas had that decision taken away from them completely, whether you realize that or not."

John nodded softly. Atlantis had not only altered their physiology but had also stripped them of their connection to their home world. If he closed his eyes he could smell the different scents of Earth from the sweat of horses in the fields to the pungent smell of aviation fuel, cordite and even the aroma of US military rations cooking in the mess tent hanging heavy over areas of the camp in Afghanistan, but these places could have been on any planet in two galaxies. His childhood memories were equally dim, with no sense of belonging in any of them, and no sense of home at all until he met a brash scientist in a bright orange fleece, and stepped into Atlantis.

He could recall his brother, Dave, with fondness. They had found some common ground after their dad's funeral, finding a way back into each other's lives. Yet, as much as John loved his brother and dearly wished to remain close to him, that familial link was weak compared to the strength of his new bond to Atlantis - and to Rodney. Rodney and Atlantis were his home now, but the strange changes meant he had no way of knowing if that had always been the case or whether it had been induced by Atlantis.

As a soldier who had been trained in Black Ops skills to deal with various interrogation methods, he knew he could not trust his current mental state no matter how much pleasure it gave him to be here in Atlantis, and to have Rodney by his side and in his bed. John knew he was compromised, and that was enough to unsettle him, perhaps even making him envious of the betas who would react favorably to the retrovirus that Carson was in the process of testing. It didn't matter what those betas decided to do after taking the treatment - return to Earth or stay on Atlantis. All that mattered was that they would be free of Atlantis's influence when they made that decision, doing so with a clear head and heart.

"So I guess you won't be taking the cure."

"On the contrary, I have a duty to take it. I simply know that it will not alter my decision to remain on Atlantis."

"Except you'll lose whatever changes Atlantis made to you. You won't be a Beta anymore."

"Yes."

John wasn't sure what a Beta felt compared to an Alpha, but if they had even the slightest additional awareness of others around them, sensing their dynamic, then it was still a lot to lose by becoming fully human again. Eventually, he knew Carson would find a cure even for the alphas and omegas, and the thought of losing his connection to Rodney sent a shiver of fear through him, but he knew he would make the same choice as Woolsey.

He would take the cure despite the heavy cost.

***

A week after the arrival of the _Daedalus_ , Carson was ready to give the retrovirus to any betas who wanted to take it, and just as he had stated to John after the briefing with Caldwell a week earlier, Woolsey stepped up first. John watched tensely, noticing the regret in Richard's eyes as he removed his jacket in preparation. Even though the betas did not experience the same depth of bond with others and with the city as the alphas and omegas, John knew from discussions that it was still there, humming at the backs of their minds. He knew Richard didn't want to lose that newfound sense of belonging in the city but John could also understand why he felt it was necessary.

"It'll take a few hours to re-code your cells back to their previous pure human state," Carson stated softly with eyes full of compassion.

From that look John suspected Richard had shared his reasons for taking the cure with Carson, including his belief that he had never had any intentions of leaving Atlantis even before gaining the beta dynamic. Richard simply felt the need to prove to Stargate Command and the I.O.A. that he was under no coercion.

The needle slipped in easily, and it was all over in seconds.

Barat stepped up next, offering a small, tight smile of apology to John before offering his arm to Carson next. Barat had replaced Bates all those years back, and he was a good man, earning respect quickly by the way he handled himself as the leader of Gate Team 6. It wasn't a first contact team but John had always been able to rely on Barat's team to back up anyone in difficulty off-world, and for providing security for the scientists working on discoveries found in Pegasus. Unlike Richard, Barat was a natural ATA gene carrier whose gene was too weak to do anything more than switch on the occasional light - and even that took a lot of concentration.

Carson had once tried to boost the strength of the ATA gene in weak gene carriers using his Gene Therapy but it had rarely made any difference, whereas the therapy worked reasonably well with those who had the gene switched off - like Rodney. It was a line of research that Carson had intended to follow up on before the events with Michael overtook him. The original Carson Beckett had not made much progress due to other priorities in the city, and John knew the clone version had been forced to continue his work on the enhanced Hoffan virus while held captive by Michael. 

After his rescue from Michael, Carson had devoted his time to trying to find a way to improve the survival rates. On Hoff, the plague had killed half the population, and Carson's vaccine had improved on that to give an eighty-four percent survival rate. The problem was making enough vaccine and getting it distributed when the plague was striking across a whole dwarf galaxy, which is why he had returned to Atlantis. Stargate Command and the I.O.A. had agreed to use Earth's resources to manufacture the vaccine, aware that the Hoffan plague was as bad as anything the Ori could have cooked up and had the potential to destroy the Milky Way too. All it took was someone breaking the strict isolation protocols and bringing the plague back to Earth with them.

He shuddered, recalling an alternate universe where Teyla had died and the whole of Pegasus had fallen to Michael. He recalled the elderly Rodney's recount of the events, and how he and Keller had left for Earth together - and how she had died months later as a result of her exposure to the Hoffan plague, on Earth. Even though he no longer felt any attachment to the planet of his birth, he realized how easily Keller might have spread the plague across Earth, and from there across the Milky Way.

John felt Rodney's presence before the infirmary door slid open to allow him entrance. Radek was with him and John frowned.

"...can't believe you want to do this?"

Radek sighed. "No, Rodney. I do not wish to do this."

Rodney looked endearingly confused. "What? Then why-?"

"As a show of solidarity to-."

"Wait! That doesn't make sense. Couldn't you show equal solidarity to those who DON'T want to take it?"

"That is why I am here. To support those who _do_ wish to take it. To show them that I respect their decision and will stand by them no matter the choice they make."

Rodney held up a finger, mouth opening and closing twice before he asked, "So... You're not taking the cure?"

"No, Rodney. When I joined the expedition many years ago, I accepted that it could be a one-way trip. I made my peace with leaving Earth. That has not changed. Atlantis is my home, and this genetic change is her way of saying I belong here now."

Unable to resist, John gravitated towards Rodney, pressing his hand against the small of Rodney's back and feeling Rodney relax against him until John's arm was wrapped around his waist. John felt a ripple of Radek's envy at their easy relationship in the air around them and for a moment, before the guilt of the situation struck him, John wished that Radek had been one of those with a strong expression of the ATA gene. Radek glanced at him perplexed, as if he had read something from John in return, but then he turned away, muttering something under his breath.

Rodney's presence lessened the tension within him as John watched the next person step up nervously to accept the treatment; John offered them warm reassurance.

"I have family back on Earth, sir," Sergeant Tomlins murmured apologetically to John.

"It's okay, sergeant. No excuses are necessary."

"Let's... not stay any longer. This is making me... anxious?" Rodney whispered, and John could feel his anxiety through the bond they shared. Or at least Rodney tried to whisper but John could tell that his voice had carried judging by the looks he gained from those closest in the small queue of betas that had formed outside of the Infirmary.

Three hours later, Richard requested John meet him at his quarters.

Almost a third of the betas had taken the cure. John knew they could have made it mandatory for all, and depending on the results, they still could, but for now it was still a choice. Those who had chosen not to take the retrovirus were like Radek, content with their lives on Atlantis. They could remember Earth and their lives back there with crystal clarity, including the emotional connection to their planet of origin, but they saw the city as their home now. Others like Richard had simply wanted to be certain that they hadn't been compromised, while the rest had reasons for wanting to go back to Earth. Those in that final group would be transported up to the _Daedalus_ as soon as it was clear that the retrovirus was working on them. Surprisingly, most of the passengers on the _Daedalus_ and seven of its crew opted to transport down to make space for those who wanted to return to Earth.

The surprise was that Caldwell allowed them to make that choice when he could have ordered them all to stay on-board.

"John. Come in."

John followed Richard out onto the balcony and accepted a shot of whiskey and a cigar with a wry smile as he sank into one of the comfortable chairs laid out in readiness. The sea and the sky were a beautiful blue and John could see the crescent shape of Lantea's moon just above the horizon reflecting sunlight; he wondered if this beauty was why the original Atlanteans had chosen this world as their home for so long. Patiently, he waited for Richard to say what was on his mind, inhaling deeply and blowing the smoke back out slowly, savoring the taste while watching the smoke curl upwards lazily. Smoking cigars was a rare indulgence, and he knew he'd catch hell from Rodney later when he smelled it on his breath and clothing, but he felt it soothe his jangled nerves. Something was wrong but he couldn't quite place his finger on it.

"It aches." Richard stated quietly before taking another draw on his own cigar.

"Carson said you might ache a-."

"I'm referring to the mental component. I no longer have a sense of those around me. Their dynamic," he added for clarity, using Carson's terminology. "I can no longer sense you're an alpha and it's... disconcerting. Like losing your sense of smell...touch... or sight. It's a feeling of missing something. Of feeling... broken inside. Alone." Richard gave a self-deprecating laugh. "I didn't believe something so... new could have such a profound impact following its loss."

John nodded, finally understanding his own disquiet since arriving in Richard's quarters. An eerie new sense of isolation sat between them, and John realized he could no longer sense Richard as a beta, worrying on his lower lip because he knew it would likely be ten times worse for him if Carson did manage to create a cure for the alphas. He would lose that sense of Rodney as his omega. He would lose that closeness.

"If you're wondering then... No. It hasn't changed my decision to stay. For now, at least."

"Good. Because I don't particularly fancy breaking in another expedition leader right now," John quipped back, hoping to break the slight strain in the air surrounding them.

Richard laughed softly and sank back in his chair, letting the silence grow more comfortable despite that strange loss of connection between them. Eventually they started talking about the city and their plans to renew contact with some of their former trading partners now they were back in Pegasus. John stayed a little longer but finally made his excuses to leave as he still had duties to perform. As he moved towards the door, Richard called his attention, and John looked back.

"John. It's not a decision to make lightly."

John knew he was referring to taking the cure if ever it became available to him. "Yeah. I know."

****

The _Daedalus_ broke orbit two days later, leaving behind a sense of finality for those betas who had stayed on Atlantis. Caldwell couldn't make any promises but he was fairly certain that the cargo runs would resume as before, with either the _Daedalus_ or the _Apollo_ bringing new or replacement people, equipment and ordnance.

That made John snort softly as he didn't expect there to be many personnel changes in future, not unless Carson found a cure for the alphas and omegas. No doubt there were soldiers and scientists back on Earth who would like to become a permanent part of the Atlantis expedition but John couldn't see Stargate Command or I.O.A. agreeing to let them come here. Unofficially, they were now under quarantine.

Over the weeks that followed, life settled back down to what passed for relatively normal. Any truly disgruntled betas had taken the cure and left the city, and those remaining seemed more content for the most part but John should have known that meant trouble looming on the horizon. 

The call came in the early hours and John groaned as he was forced to roll away from the warm body in his arms to grab his radio. He heard Rodney's rumble of disapproval, smiling slightly as Rodney rolled in his sleep, hand reaching out to draw him back. The large, sleep-warmed hand landing softly on his thigh sent a surge of desire through him, mingling with the mellow warmth of love and the intense need to cherish and protect his bonded mate. It took every ounce of willpower not to ease back into Rodney's arms and slake the hunger that was physical, mental and emotional. He resisted the temptation, slotted the tiny radio into place and tapped the ear piece.

"Sheppard."

"Sorry to wake you but we have a situation, sir." Lorne's voice seemed tight. "Level 3 civilian quarters."

"On my way."

A sleep-heavy voice caught him before he could leave the bed. "John?"

Leaning over, John kissed Rodney gently, momentarily allowing the bond to send its warmth through him before drawing back. He knew Rodney had come to bed late last night, working more closely than ever with Atlantis these days in repairing her systems. Rodney had always had an uncanny ability to understand Atlantis but since becoming an omega, his link to the city had increased tenfold.

He nuzzled his cheek against Rodney and whispered, "Go back to sleep," before climbing out of bed and dressing quickly. If Lorne needed Rodney then he would have called him too.

Atlantis had always tended to obey John's mental 'requests' quickly but now the city seemed to anticipate him, opening doors ahead of him and even selecting the destination before his fingers had touched the panel at the back of the transporter. The doors slid open onto another corridor in the area set aside for the scientists' quarters and John could see a dozen or more scientists and soldiers milling about ahead, gathered in small groups. He could sense a mixture of dynamics, recognizing at least one pair-bond.

Lorne, looking grim-faced, stepped aside to allow John to enter the quarters of Doctor Bencot. John's footsteps faltered when he spotted Keller kneeling beside an unconscious woman, tending to her injuries. He recognized Sergeant Freemond, who was on the floor on the other side of Bencot, kneeling in the pool of blood from a head wound and holding Bencot's hand tightly, his fingers entangled with hers. All of his focus was on the petite woman, as if nothing else existed outside of her. John caught Keller giving Freemond a worried glance but otherwise, she made no request for him to move aside.

"What happened here, Lorne?"

"From what I can gather, Doctor Bencot was in a relationship with Doctor Gartel... until a few weeks ago when she bonded with Sergeant Freemond."

As he listened to Lorne's report, he berated himself internally. He should have anticipated something like this happening and he wondered how many other relationships - requited or otherwise - had been torn about by the strange genetic changes. Rodney had planned to marry Keller before she felt that compulsive attraction to Ronon, and if Rodney had not been feeling a similar attraction to him then it might have bothered Rodney a whole lot more. There were a few other cases, and Ronon had overheard one woman lamenting the fact that ' _the Colonel_ ' was now unavailable, referring to his exclusive bond with Rodney. 

"So where's Gartel?"

"Gartel is locked up in the Wraith cell."

"And Freemond?" He indicated towards the distraught man, feeling his own chest tighten at the sight; Lorne looked equally tense.

"David always seems to know when I've been hurt so I can only imagine how Freemond feels right now."

"Freemond's the omega?"

John raised an eyebrow in surprise because it tore apart all the theories that becoming an alpha or omega was related to dominant or submissive qualities, and once again John wished Carson hadn't used those particular tags for each group. When people heard the words Alpha, Beta and Omega they immediately associated it with wolf packs and the dynamics between members of the pack. Originally Carson had believed it was related but as the weeks passed, he determined that this was not the case here on Atlantis. There were betas and omegas who were dominant types, like Richard and, yes, Rodney and Carson. And now here was an alpha who - to John's memory - had seemed physically weak and even quite timid before the strange changes, but who was bonded to an omega who had to be one of the toughest marines under John's command.

Only Atlantis knew why each individual had altered to their particular dynamic, having orchestrated it. Some suspected it was more of a matchmaking exercise for the Atlantis A.I., with Atlantis wanting to ensure the continuance of the ATA gene by bonding only carriers of the gene with each other. However, that theory fell over when they took into account the bonds that had formed between two individuals of the same gender. It wasn't like he and Rodney were going to be able to start a family with each other, so if procreation had been Atlantis's sole intent then the city would have paired male and female together in all cases.

John watched as the medical team moved Bencot to a gurney and he followed on behind as they headed off to the infirmary. He knew the medical doctors would tell him what he needed to know when they were ready but Keller didn't seem too anxious, and by the time they reached the infirmary, John could see Bencot stirring on the gurney. This time Keller asked Freemond to stand aside, and John thought he might have to make that an order when Freemond hesitated.

"Sergeant Freemond. A word."

Freemond looked torn between obeying and remaining close to Bencot but duty won out.

"What happened?"

"Gartel happened," he spat out. John watched as Freemond visibly pulled himself back under control. "Sorry, sir. Gartel wasn't too happy when Yvie turned alpha and chose me." He snorted softly. "Still being ribbed about that by the guys, about how Yvie is the alpha in this bond, but anyone who really knew her wouldn't be so surprised. She's little but she's scrappy, and she knows what she wants, and I'd seen her put a few others in their place even before the... change."

The curtain swished open before John could push Freemond back on track about the incident with Gartel, but John felt the tightness in his chest loosen when Freemond smiled, tension flowing out of him as he rushed across the room to his Yvie. John blinked, realizing that what he'd been reacting to was Freemond's distress. Glancing around, he caught Lorne's eyes and knew he wasn't the only one who had felt uptight and anxious. He wondered if this was another side to the changes, that alphas could feel an echo of this protective urge towards all omegas, and not just to their own bonded mate.

John followed Freemond over to the bedside and smiled down at Bencot, who was looking pale but alert. He listened in as Keller explained that Yvie Bencot had a concussion and would need to remain under observation for the next 24 hours.

"Are you up for answering a few questions?" John asked softly, prepared to back off if necessary and turn his attention to Gartel. It would help to go into the interview with her version of the events leading up to the incident and the cause of her injuries.

Bencot nodded but the way she screwed up her eyes and then hissed proved she regretted both actions immediately. A stark white bandage hid the gash on the right side of her forehead but not the bruise across her left cheek bone and eye. John had seen enough of these types of injuries - usually in training exercises - to know that it was likely caused by a fist, and she'd probably impacted her head when she fell.

"Kevin's an alpha and I guess he just assumed that as I had the gene too, that I'd be his omega... especially when none of the omegas felt any attraction to him."

John prompted her when she fell silent, drifting away within her own thoughts. "But it didn't work out that way?"

This time she caught herself before shaking her head. "No." Her eyes drifted to the man seated beside her, holding her small hand in his; she smiled softly. "Greg was always looking after me off-world. He would be the first to offer to help carry my equipment, and he'd watch over me as I set it up. He'd bring me coffee and sandwiches when I got so caught up I forgot to eat." Her smile widened as his fingers tightened on hers, and John could sense the joy and love in their bonding, seeing a reflection of his own bond of love and friendship with Rodney - though in reverse. "I was so shocked when Greg turned out to be my omega... but pleased."

"Not half as shocked as me," Freemond retorted with a wide smile.

"Back to Gartel," John said. "I gather he didn't take it too well when you bonded with Sergeant Freemond."

"No. He kept pestering me, trying to get me to touch him in some belief that I would spontaneously turn omega... just for him." She closed her eyes and moaned softly in pain; John saw Keller hovering, ready to call a halt to the interview. "Usually Greg was there to fend him off but last night..."

"I was on sentry duty, sir."

John nodded, having learned that from Lorne earlier. He indicated for Bencot to continue.

"He said he just wanted to talk, so I let him in. When he tried to kiss me, I pushed him away hard and slapped his face. He hit me back, and that's all I can remember until I woke up here. I don't know how I hurt my head."

"There was blood on the edge of the dresser. I think he hit you hard enough to knock you off your feet, and you struck your head on the way down." 

Keller was starting to loom over them now so John decided he had enough information to take to Richard. He knew Richard would want to be involved in the interview with Gartel even though the new Lantean forces were no longer strictly military. They now fulfilled the equivalent of a civilian law enforcement role too, and Richard had insisted on amendments to the uniform code to balance those changes, especially within Atlantis.

The rest of the day passed by in a blur of interviews and debates.

Gartel admitted to striking Bencot, and John would let Richard decide how they would proceed. He knew Richard was going over all the paperwork Elizabeth had left behind in the event that Atlantis lost contact with the Milky Way and became a colony. He knew Richard had his own ideas too, and setting up a new charter took greater priority now that they couldn't simply hand Gartel over to the _Daedalus_ or _Apollo_ , whichever arrived first, for transport back to Earth to stand trial. This was _their_ problem now.

He was surprised to find Rodney already asleep in their bed when he finally returned to their shared quarters, until he checked the time and realized it was three in the morning. With a sigh, John undressed quietly and slid into the bed beside Rodney, smiling when Rodney grumbled about how cold he was - though that didn't stop him from attaching himself to John like a limpet.

It took a while to shut off his tired brain but, eventually John fell asleep to the sound of Rodney's quiet snuffles.

****

The next two Lantean months went by swiftly without any similar incidents, and with the agreement that Gartel would remain in the Wraith cell under guard for one week, and would then be monitored for a further three weeks while undergoing counseling sessions. It wasn't ideal but John didn't want to waste the manpower when Rodney had already figured out a way for Atlantis to ensure Gartel obeyed the ' _restraining order_ ' that meant he wasn't allowed within thirty feet of either Bencot or Freemond until the restraint was lifted.

Eventually a more serious crime would be committed that couldn't be handled in the same way. If the perpetrator was a beta then the solution was easy enough. They would be given the ' _cure_ ' and sent back to Earth, but until today the same could not apply to alphas or omegas.

Carson was understandably grim-faced as he presented his ' _alpha/omega cure_ ', aware that if Stargate Command got a hold of it then they might force it on the alphas and omegas on Atlantis. John could understand Carson's reticence because he had seen his work bring destruction in the form of the Hoffan plague, and he could think of no one who would willingly take it, including himself. All of them were compromised, and for that reason alone John felt unwilling but duty-bound to take the cure. Yet he had never been happier in his life than he was now, here in Atlantis with his bonded mate by his side. The thought of giving all of that up was tearing him apart but he could see no other solution. He needed to know if this was all just a fantasy created by Atlantis, and if he would still feel the same about his life here on Atlantis once it was his own choice.

"John, you don't have to do this."

John could feel Rodney's distress through their bond and he hated being the one to cause it. "I have to," he whispered back, barely able to voice the words that were crushing Rodney's spirit.

"I don't want-." Rodney started and John hushed him with a kiss.

"I know."

He watched as Rodney pulled back and drew himself up, straightening his shoulders. "But if you go through with this, then I will too."

"You don't have to."

"Yes. Yes, I do."

John could see the obstinate set of his mouth and knew Rodney had made up his mind, giving him the ultimatum perhaps in the hope that John would change his mind about taking the cure.

"Why?"

He saw the broad shoulders sag. "Because once you're no longer an alpha, but I'm still an omega, I might end up bonded to another alpha. I don't want to forget how much you mean to me right now."

John felt a ripple of shock go through him, having never considered that possibility. He felt physically sick at the prospect of losing Rodney to another, understanding how Gartel must have felt when he lost Bencot to Freemond. Admittedly it wasn't quite the same due to the dynamics but it was close enough. He wondered if he could stand to see Rodney in the arms of another alpha; to see him gazing with love and affection into someone else's eyes, touching and loving someone other than him. He steeled himself.

"I have to," he stated softly, answering the silent cry to not do this to them, and looked away when Rodney closed his eyes, already anticipating the loss.

Rodney was resistant when John drew him into another kiss but slowly thawed in John's arms, sagging against him as John drew him to their bed and they made love slowly. He took his time to explore every inch of skin, wanting to memorize every second, every caress, and every hazy, warm sensation that rippled through the bonding link. When he pushed slowly into Rodney, he gasped at the bright flare of the bond that seemed to set his blood on fire with need and desire. He felt Rodney's legs wrap around him, holding him tight, and pulling him in harder and deeper. When he came, he felt that momentary union of his mind with Rodney's, sharing every thought and sensation for an instant in time before he was falling back into himself.

He left while Rodney was still asleep, heading for the infirmary where Carson was waiting.

"I was hoping you'd changed your mind," Carson sighed as he prepared the shot. He paused with the needle poised against John's skin, blue eyes cutting deep into his and silently pleading with him to let this go.

"Do it," John ordered, and gritted his teeth as the needle sank into his skin, and Carson released the contents of the syringe into his vein. It was done in seconds.

"It will take a few hours before you notice any changes. If you want-."

Rodney burst into the infirmary, eyes wide and zeroing in immediately on the way John's arm was bent at the elbow, holding he small cotton wall pad in place at the injection site. He straightened his shoulders and walked forward stiffly, taking a seat on the medtable opposite John.

"Carson."

"Rodney... No, lad. You don't have to-."

"I do."

With a bitter smile, Carson prepared another syringe but as he tapped the vein to bring it up, the Atlantis biohazard warning sounded in the infirmary. Carson put down the syringe and went to the console, wanting to know why Atlantis had raised an alarm. He frowned as he scrolled through the data, suddenly turning his head to look right at Rodney.

"I need to do a full body scan, Rodney."

"What is it?" John demanded but Carson merely held up a hand.

"Rodney," Carson insisted, and John watched as Rodney followed Carson across the infirmary, finally levering himself up to join them as Rodney lay down on the scanner bed.

By now Keller had arrived, probably alerted by Atlantis, and he glanced across at her, wondering why he still called her Keller when she was bonded to one of his best friends. It wasn't as if she could take Rodney away from him anymore, and he'd helped Ronon celebrate his impending fatherhood only a few days earlier, which sealed the bond between Ronon and... Jennifer.

"Is that...?" Her words broke off as she studied the image with Carson, her eyes wide in genuine surprise or shock. John couldn't tell which.

"I need to run a full series of tests but... Yes."

"I realize medicine is a fascination to you so it may have escaped your notice that I'm lying right here, Carson. What is it? Is it a tumor? Am I dying?" Carson looked up at him with wide, blue eyes. "Oh God! It is! I've got cancer! This is your fault, Sheppard! I knew flying too close to that sun all those years ago would send my lifetime exposure over the limit."

Carson frowned, blinking rapidly. "You don't have cancer, and you're not dying, Rodney."

"Then what is it?" John demanded again.

Carson flicked his eyes towards John, and John could read the shock in them before Carson looked back at Rodney. "Rodney? You're... pregnant."

For a moment the silence was broken only by the small electronic sounds and background hum of the infirmary, before Rodney rolled his eyes and began to laugh harshly, shaking his head.

"Of all the excuses you could have come up with, you went with that? I know you didn't want me to take the cure but..." Rodney trailed off when Carson stared back up at the holographic image above the scanner bed.

John joined him, but he hadn't a clue what he was looking for until the image zoomed in on the tiny bundle of cells that was forming a new life inside of Rodney. A baby. His baby.

John looked down at his hand still pressing the cotton wadding against the injection site from where he'd taken the cure.

"No," he whispered, realizing it was too late for him to change his mind.

*****

John felt the bond between him and Rodney slowly die as his body returned to its former human state. His memories of Earth returned fully, along with all the emotions connected with the planet of his birth, and yet nothing changed for him. He felt no sudden desire to return to Earth nor renewed sense of duty to Stargate Command that surpassed his loyalty towards Atlantis and people in the city. He felt only an overwhelming sense of loss instead as he wandered through the corridors of Atlantis, no longer able to feel that deep connection to the city or to the others - alpha, beta or omega.

"Sir?" Lorne looked uncomfortable as he approached John, and he wasn't the only one.

John could see the discomfort with his loss of dynamic reflected back at him from many others too, with some openly avoiding him. Now, he truly understood how Richard and others had felt in Atlantis since taking the beta cure yet remaining here. Like him they had needed to be sure that they were not compromised but this sense of loss was shocking, and almost unbearable.

John's ATA gene was still as strong as before, even if he no longer felt the same connection to the city, but that didn't dull the ache in his heart and mind from where the slender bond to the city and, more importantly to Rodney had once vibrated through him. He could see that same loss on Rodney's face, aware that Rodney was barely holding it together - and then only because he was at least physically present.

Carson likened it to a form of grief.

That first night he had clung to Rodney so tightly, and Rodney's hands had left bruises where he had held him in an almost brutal grip, neither of them coping well with the loss of their bond. John felt as if a huge part of him had been ripped out, and he could only imagine that Rodney felt the same.

Over those first few days, John could barely be apart from Rodney, dreading every time one of the unbonded alphas came close enough to touch Rodney in case Atlantis - or whatever chemistry governed the bonding process - decided that one of these alphas should replace John. He only started to relax once he was certain that this wasn't going to happen, but that relief was short-lived. 

A month after taking the Alpha cure, the _Daedalus_ slid back into orbit above the city and began to beam down supplies. When Caldwell informed Richard that he had passengers to beam down as well - ones who wanted to become a permanent part of Atlantis and were willing to accept any genetic changes - John felt anxious once more. If these newcomers were affected by Atlantis then most of them would become betas, but there was always the possibility of one or two becoming alpha or omega. Not even the knowledge that their physiology might be changed radically enough for a male omega to fall pregnant was a sufficient deterrent for those with stronger expressions of the ATA gene, whether naturally or gained through the original gene therapy.

"Sir?" Lorne called again and John looked up from his paperwork to find Lorne hovering on the threshold of his office, still a little uncomfortable in his presence.

After taking the beta cure, Sergeant Barat had left on the _Daedalus_ leaving only the Lantean military, and even though John no longer had a dynamic, Woolsey had refused to relieve him of his duty as Commanding Officer on Atlantis. Lorne had felt the same way and the respect John had garnered over the years from the men under his command meant there was no dissension in the ranks. Alpha or human, they were content for him to remain in command.

"Major."

"The new personnel are ready to beam down."

John nodded tightly, feeling a sense of dread in the pit of his stomach. When he reached the gate room, Rodney was already standing by the upstairs balcony rail, looking slightly agitated, with Carson and Jennifer waiting beside him. John didn't make his presence known immediately, aware that they would not sense his approach now he no longer had an alpha - or any dynamic.

"Not that I'm unhappy with the situation, Carson, but can you come up with any plausible, non-voodoo reason why none of the unbonded alphas were attracted to me?"

"To be truthful, Rodney, we know so little about the changes. Obviously there are pheromones being produced by omegas that attract a certain alpha. In my case it was Laura, and in Jennifer's it was Ronon."

"And in mine it was John," Rodney added bitterly.

"Aye." Carson sighed. "If those alphas were not compatible with you before you bonded with John, then they will still not be compatible now."

"But a new alpha from the _Daedalus_ might be," Jennifer added brightly. Her smile faded when she realized that she had misunderstood Rodney's concerns, and she looked even more apologetic when she glanced over her shoulder and met John's eyes. "Or not," she added hastily.

Carson looked apologetic too. "Well, we won't know for a few weeks... if they change at all."

"The others did," Rodney stated mulishly, referring to the ones who had arrived on the _Daedalus_ several months earlier.

"Aye, they did."

What was uppermost in John's thoughts though was that three months had passed since Richard took the cure and Carson had seen no sign of his beta dynamic returning. Without realizing it at the time, John had held onto the slender hope that Atlantis would revert him back to an alpha if he remained in the city after taking the cure. As the days turned into weeks, he felt that hope slip further away.

The light from the Asgard transport beam caught his attention and he watched as a several groups appeared in quick succession, surprised when one of them was Colonel Caldwell. Rapidly, John moved down the main staircase to the lower level.

"Colonel?"

"Colonel." 

Any remaining hope shattered when Caldwell greeted him back with a slight dip of his head, his presence confirming that the quarantine restrictions had been lifted. It meant Carson was confident that the cure worked - permanently - even though only John and three others had taken the alpha-omega version. The rest were content to remain alphas and omegas, and John knew for a fact that all four of them regretted their decision, along with all the betas who were now human again but still in Atlantis.

All that remained now was to see whether Earth would insist on everyone taking the cure, but the new Lanteans had already voted to secede from Earth rather than give up their dynamic. John hoped Caldwell wasn't going to be the bringer of bad news because Caldwell had pulled his and his team's collective ass out of the fire a number of times and he'd grown to like him over the years. He would hate to see them lose that mutual respect.

He watched as Caldwell flicked a glance up towards Rodney but there was no disgust in his eyes, only curiosity. Rodney wasn't the only omega male who was carrying his alpha's child. What had surprised John most was learning that Sergeant Freemond was also pregnant instead of his ' _wife_ ' Yvie Bencot - but not Carson. It turned out that Bencot had a serious accident as a child and would never be able to bear children. It seemed Atlantis had decided on the perfect solution in their case as well as for the same gender couples like him and Rodney.

His heart ached again as he thought of Lorne and his partner, Parrish, and how their expected child had brought them even closer together.

He could have had that with Rodney instead of this constant fear of losing his partner. He could have felt the growing child through their bond, sharing in their impending fatherhood but instead, all he felt was emptiness. They still slept together, still held each other close and had great sex. Rodney insisted it was enough and John believed him, but that didn't stop him from worrying that one day Atlantis would give Rodney a new alpha and he would end up like Gartel - watching the person he loved bond with another.

The _Daedalus_ stayed on Atlantis for a week before heading back to Earth. What surprised John most was that Caldwell didn't go back with his ship.

****

Almost a month after the _Daedalus_ left for Earth, John was sitting opposite Rodney in the mess hall when Doctor Stevens slipped and grabbed for the first handhold available, which happened to be Rodney. His cry of pain and twist out of her unintentional grasp sent both of them crashing to the floor. John was on his feet instantly and half way around the table before he registered what had happened. He snatched his hand back before it could touch Rodney's skin, feeling sick inside.

In all his studies of their new dynamics, Carson had discovered only one thing that could make an omega's skin excruciatingly painful to touch from all but one individual.

The formation of a pre-bond.

Rodney stared back up at John in shock, neither of them hearing Stevens' stumbling apology. John reached out a hand towards Rodney again but drew it back, fingers curling inwards into a fist. He straightened, feeling even more broken inside at the realization that his worst fear had come to pass. He had lost Rodney to another.

"John?"

Rodney's single choked word tore at John as he turned and walked away.

Not wanting to hurt Rodney with his own touch, and feel that final blow when Rodney pulled away from him as if burned, John moved out of their shared quarters and stayed as far away from Rodney as humanly possible. Another month went by slowly - torturously - and whenever they were in the same room he found his eyes gravitating to Rodney's thickening middle - their child. He made certain they were never alone together, and never in close proximity, waiting for the day when Rodney would no longer seek him out across the room, being too intent on the new alpha in his life.

John looked up when he heard a heavy sigh from someone hovering at his office door, and gave his own internal equivalent of a sigh when he saw it was Carson.

"John?"

He forced a smile onto his face. "Doc. How can I help you?"

"By not being an ass and go see Rodney."

"You know I can't do that," he whispered back, even though every cell in his body wanted to be with Rodney. He'd had his chance and he had thrown it all away in the name of duty.

"Caldwell was the only new alpha from the last bunch from the _Daedalus_. He's just formed an alpha-omega bond."

John felt his heart break at that news. He hadn't known Caldwell had the ATA gene, let alone strong enough to change to an alpha or omega dynamic. But if he was the only new alpha, then it meant he was Rodney's new alpha. John tried not to let his grief show on his face as he smiled up at Carson.

"But he's not Rodney's alpha," Carson added. "None of the unbonded alphas currently residing in the city are attracted to Rodney." Before John could air his confusion, Carson continued. "For God's sake, man. I need you to touch Rodney."

John shoved to his feet in anger. "What? No! I... can't hurt him any more than I already-."

"You're both miserable... and I have a suspicion that-."

"John."

John snapped his head round as he heard Rodney call his name. Before he could move, Carson stepped out of John's office and shut the door behind him, leaving John alone with Rodney, and with only the desk standing between them.

"As much as it pains me to say this, especially as neither of us are the poster child for heart to heart discussions... We need to talk."

"I don't think so."

"Fine. Then I'll talk and you can listen." Rodney took a deep breath. "Caldwell bonded with Woolsey."

"What?"

"Richard's dynamic came back... except... not." He waggled his fingers in an almost obscene gesture. "It's all voodoo Carson-speak but his dynamic came back as an omega. Something about the cure altering his genetics enough to strengthen his extremely weak, recessive ATA gene so when Atlantis altered him again..." Rodney huffed, shoulders set as he approached the desk. "The point is, John. His dynamic came back."

John felt a flare of hope but viciously quashed it before it gained too strong a foothold. 

"So you're thinking... if Woolsey's dynamic can return then so can mine?"

By now Rodney was halfway round the desk. "Yes. Yes, I am."

"I have news for you, Rodney. I don't sense an omega in this room. I don't sense anyone," he added bitterly, anger raising his voice.

"But I sense you!" Rodney snapped back furiously, reaching for John only for his hand to be slapped away.

The shock of that touch went straight through John, burning with an intensity that he'd mourned since its loss five months earlier. With it came an almost overwhelming sense of completeness that John had also thought lost forever after taking the cure. Hesitantly, he reached out again to touch Rodney, just to prove to himself that it had happened, and with this touch his alpha dynamic surged back fully. It felt like that first time all over again, with a desperation to feel skin against skin. He was barely aware of losing his clothing, caught in the throes of passion as he devoured Rodney's mouth in hungry, needy kisses.

Some part of his mind registered the crash of papers, trays and his laptop hitting the floor as Rodney sprawled back across the desk but he didn't care. He needed the man beneath him more than he needed air to breath, and as he sank into Rodney's body, he felt the ragged ends of the torn bond healing and strengthening, sensing not just Rodney but also the child he carried. Their child.

A small knock on the door registered less than an hour later, and John was so glad he was aware enough to investigate as someone had piled up supplies by the door including food, water and a rolled-up mattress with warm blankets. He dragged it all in and locked the door behind him, glad to get off the hard but, thankfully, warm floor.

"Remind me to thank Carson... or whoever left us a mattress," Rodney groaned as he stretched out on the bed they had quickly made up on the floor of John's office. He dragged John down beside him, wrapping his arms and legs around his bonded mate as he lay his head on John's shoulder. The mental and physical exhaustion of the last few months crashed down on both of them... and John slept well for the first time since taking the cure, safe and happy with Rodney in his arms.

When he awoke, any lingering fears vanished at the feel of the bond singing between them, and he lost himself in Rodney again... and again.

****

 **Epilogue:**

Within the space of a few weeks, the city filled with the cries of newborns as a new generation of Lanteans came into the world. John sat beside Rodney in the infirmary, holding his equally nervous bonded mate's hand as Carson and his medical team made their final preparations. He was about to become a father, and twenty minutes later, when Carson placed the crying newborn into his arms, John could barely catch his breath as the little boy fell silent, staring up at him. He carried their son to Rodney, placing him in Rodney's arms but letting his hands lay gently on both Rodney and their child.

The bond between them shimmered, bright and golden, as they became a family.

END

**Works inspired by this one:**

  * [Art and Fanmix for "Compromised Positions"](https://archiveofourown.org/works/1215589) by [Gryph](https://archiveofourown.org/users/Gryph/pseuds/Gryph)




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